Re: [AMBER] ligand force field

From: Matias Machado <>
Date: Fri, 09 Nov 2018 12:41:26 -0300 (UYT)

Dear Hosein,

These observations aren't correct, loading residues from a lib doesn't imply that you have to use them and by no mean extra residues is going to be added to the system just because they are present in a lib file and not in you input PDB... just think in the case of ff14SB, which contains topologies for all amino acids but still you use it to represent proteins which may not have all of them...



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "hosein geraili" <>
Enviados: Viernes, 2 de Noviembre 2018 15:22:13
Asunto: [AMBER] ligand force field

I used force field parameters from an article for a ligand inside a protein, so I created the ligand.lib and ligand.frcmod files, now I wanna use these files along with the main pdb file of the protein which has the ligand inside, and load this pdb, ligand.lib, and ligand.frcmod in tleap to get the .prmtop and .inpcrd for all the atoms, but the problem is if I retain the ligand atoms inside the pdb file in the final .inpcrd and .prmtop there will be two ligand, and if I delete all the ligand atoms from the pdb file, there will be no ligand in the final .prmtop and .inpcrd.Any comment on that??Best
AMBER mailing list

AMBER mailing list
Received on Fri Nov 09 2018 - 08:00:04 PST
Custom Search